tbuckley/cabot-search huggingface dataset:
PATH-64. COMPREHENSIVE CNS TUMOUR MOLECULAR DIAGNOSTICS USING THIRD GENERATION SEQUENCING
Authors: Areeba Patel, Felix Hinz, Helin Dogan, Kirsten Goebel, Daniel Schrimpf, Pauline Goeller, Michael Ritter, Lisa Pfeifer, Christina Blume, Natalie Berghaus, Alexander Payne, Violaine Goidts, Matthew Loose, Andreas Unterberg, Wolfgang Wick, Stefan Pfister, Martin Sill, Andreas von Deimling, David Jones, Matthias Schlesner, Felix Sahm
Journal: Neuro-Oncology (2023)

Abstract The WHO classification of CNS tumours 2021 recommends reporting a wide range of molecular alterations for WHO-compatible diagnoses. Conventional workflows warrant considerable investment and long turnaround times limited by batching. Nanopore sequencing enables long read sequencing, real-time targeting and simultaneous base modification detection with compact devices. Rapid-CNS2- a rapid, comprehensive adaptive sampling based sequencing pipeline with a turnaround time of 5 days was previously described. The ad-hoc methylation classification model employed by Rapid-CNS2 is limited to MNP v11 classes. This study presents an optimised Rapid-CNS2 and validation cohort that successfully reports hard-to-detect variants. We also present a whole genome sequencing workflow that affords direct upload to the MNP website for MNP v12 classification. We sequenced and analysed 156 samples from the Department of Neuropathology, University Hospital Heidelberg using Rapid-CNS2. RESULTS: were compared to NGS panel sequencing and methylation array analyses. Rapid-CNS2 showed improved resolution over NGS panel sequencing for CNAs. High accuracy was obtained for detection of SNV/Indels. Long reads spanning the breakpoint identified clinically relevant fusions in 10/10 cases. Subclonal SVs like EGFR vIII missed by NGS panel sequencing were detected with high confidence. Complete concordance was achieved for MGMT promoter methylation status and methylation classification for MNP v11 classes. The optimized Rapid-CNS2 workflow shortened the turnaround time to 30 hours from sample receipt and minimum input DNA required was reduced to 500ng. For WGS, samples were sequenced for 72h on a Promethion device. WGS enabled accurate reporting of SNVs, CNAs, SVs, MGMT promoter status in addition to MNP v12 classification directly from the website eliminating the need for ad-hoc training of methylation classification models. The presented nanopore sequencing based workflows provide feasible single assay alternatives to conventional molecular diagnostic approaches with the aim to make such analyses more accessible.
RTID-03. A PHASE 1/2 STUDY OF THE WEE1 INHIBITOR DEBIO 0123 IN COMBINATION WITH TEMOZOLOMIDE +- RADIOTHERAPY IN ADULTS WITH RECURRENT OR NEWLY DIAGNOSED GLIOBLASTOMA
Authors: Patrick Roth, Kyriakos P Papadopoulos, Maria Vieito, Jonathan Yang, Nazanin Majd, Juan Sepúlveda, Lauren Schaff, Victor Moreno, Jaime Gállego Pérez -Larraya, Sandrine Micallef, Anne Bellon, Mokhtar Omar, Esteban Rodrigo Imedio, Luke Piggott, Victor Rodriguez-Freixinos, Jordi Rodon
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND: Debio 0123 is an oral, brain-penetrant, highly selective WEE1 inhibitor. WEE1 inhibition leads to S phase and G2/M cell cycle checkpoint abrogation, permitting mitosis without DNA repair, leading to mitotic catastrophe and subsequent cell death. Preclinically, Debio 0123 has been shown to effectively penetrate the brain and demonstrated improved response to radiotherapy (RT) in vitro and temozolomide (TMZ) in mouse models of GBM, supporting the clinical investigation of Debio 0123 with TMZ +/- RT. Trial design: This Phase 1/2 multi-center study (NCT05765812) is evaluating Debio 0123 in combination with TMZ in patients (pts) with recurrent GBM isocitrate dehydrogenase (IDH)-wildtype (WT) or astrocytoma, IDH-mutant, Grade 3 (per WHO 2021 criteria) after first-line, TMZ-based chemoradiotherapy (CxRT) (Phase 1 Arm A) and Debio 0123 combined with TMZ-based CxRT in pts with newly diagnosed GBM IDH-WT (Phase 1 Arm B). In Arm A, pts will receive escalating doses of Debio 0123 with TMZ in 28-day cycles supported by a Bayesian logistic regression model (BLRM). Arm B is a Debio 0123 dose escalation with concomitant TMZ/RT for up to 6 weeks. The primary objective of both Phase 1 arms is to identify the recommended Phase 2 dose (RP2D). Secondary objectives include safety, pharmacokinetics, and preliminary antitumor activity. Key inclusion criteria are ≤2 prior treatment lines (only 1 systemic line allowed) and Karnofsky Performance Status (KPS) ≥60 (Phase 1 Arm A). In Phase 1 Arm B, pts with KPS ≥70 who are eligible for standard TMZ-based CxRT will be included. Phase 2 will be an externally controlled, open-label study comparing the efficacy (overall survival) of Debio 0123 combined with TMZ at the Phase 1 Arm A RP2D vs. standard of care in pts with recurrent GBM IDH-WT. The control arm will include patient-level data from recently completed clinical trials. Accrual is currently ongoing.
TMIC-28. TARGETING TUMOR-ASSOCIATED SMOOTH MUSCLE ACTIN (ACTA2) EXPRESSION IN MOUSE PRE-CLINICAL GLIOMA MODELS REDUCES TUMOR PROGRESSION AND EXTENDS SURVIVAL
Authors: Andrea Comba, Maria Luisa Varela, Cliford Abel II, Syed Faisal, Maria Castro, Pedro Lowenstein
Journal: Neuro-Oncology (2023)

Abstract The ACTA2 gene, which encodes α-smooth-muscle actin, is known to be involved in contractility and oncogenic transformation. However, the specific role of tumor-associated ACTA2 mesenchymal cells in gliomas is unknown. Using genetically engineered mouse models (GEMM) of glioma, we discovered that ACTA2 expression was increased within oncostreams, which are malignant multicellular structures found in high-grade gliomas. Furthermore, we observed reduced expression of ACAT2 mRNA in IDH-Mut mouse gliomas vs WT tumors. Analyzing human glioma TCGA and CCGA databases revealed a negative correlation between tumor ACTA2 expression and overall survival in glioma patients. ACTA2 mRNA expression was also higher in grade IV and recurrent tumors. To investigate the role of ACTA2 in glioma cells, we created ACTA2 knockdown GEMM of glioma. These mice showed very large increases (~300%) in median survival (NPDS: 253 days, NPAS: 329 days) in comparison to their respective control groups (NPD: 89 days, NPA: 97 days). Glioma neurospheres derived from knockdown tumors confirmed downregulation of ACTA2, and showed reduced cell proliferation compared to controls. Moreover, orthotopic models revealed a decreased potential for tumor development in vivo. To explore the mechanism mediating the effects of ACTA2 downregulation, we conducted RNA-Seq analysis of ACTA2 knockdown neurospheres. This analysis identified approximately 5000 differentially expressed genes, with gene ontology analysis highlighting significant enrichment in biological processes such as cell adhesion, cell communication, and regulation of locomotion. Pathway analysis identified cytokine-receptor interactions, focal adhesion, and NFK-B signaling as the most significant signaling pathways affected by ACTA2 downregulation. Finally, we evaluated the release of cytokines into the cell-conditioned media and found significantly decreased levels of GSCF and GMSCF cytokines in ACTA2 knockdown compared to controls. These findings indicate that ACTA2 expression is a pro-tumoral gene involved in glioma progression and plays an essential role in altering the TME.
CTIM-32. A PARALLEL COHORT PHASE 2 STUDY OF REGORAFENIB PLUS NIVOLUMAB FOR RECURRENT OR METASTATIC SOLID TUMORS: RESULTS IN PATIENTS WITH GLIOBLASTOMA MULTIFORME (GBM) OR ANAPLASTIC ASTROCYTOMA (AA)
Authors: Matteo Simonelli, Mario Caccese, Delphine Larrieu-Ciron, Enrico Franceschi, Tae Min Kim, Jerome Fayette, Pierre Freres, Marie Robert, Marica Eoli, Sylvie Luce, Jana Portnow, Yuki Hirata, Kengo Enya, Ian Waxman, Lixian Jin, Dipam Shah, Uta Drews, Marie-Aude Le Berre, Giuseppe Lombardi
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION The multikinase inhibitor regorafenib improved overall survival (OS) versus lomustine in relapsed GBM in the randomized phase 2 REGOMA study. The aim of this study was to evaluate the efficacy of regorafenib combined with nivolumab in this setting (NCT04704154). METHODS Patients aged ≥ 18 years with recurrent GBM/AA (WHO 2016 classification) after radiotherapy plus temozolomide, and an ECOG performance status (PS) of 0/1, received oral regorafenib 90 mg/day on days 1–21 and intravenous nivolumab 480 mg on day 1 of each 28-day cycle. If tolerated, the regorafenib dose could be escalated to 120 mg/day from cycle 2. Prior regorafenib treatment or immunotherapy was not allowed. The primary endpoint was objective response rate (ORR) using RANO criteria. Secondary endpoints included progression-free survival (PFS), OS, and safety (MedDRA; CTCAE v5.0). RESULTS Of the 36 patients enrolled, 30 were treated and were eligible for analysis. Median age was 60 years, 63% had an ECOG PS of 1, and 90% had GBM (10% AA). All patients discontinued treatment as of the primary analysis (March 9, 2023). One patient had a best-overall partial response (ORR; 3%) and nine (30%) had stable disease. Median number of cycles of regorafenib and nivolumab infusions was three. Median PFS (RANO) was 2.7 months (80% CI 1.8, 7.3) and 6-month PFS was 31.5%. Median OS was 8.0 months (80% CI 4.6, 12.4) and 12-month OS was 33.7%. Thirteen patients (43%) had grade 3/4 treatment-emergent adverse events (TEAEs), which were drug-related in 12 patients (40%). The most common drug-related grade 3/4 TEAEs were AST increase (13%), ALT increase (10%), and hypertension (10%). There were no immune-mediated serious TEAEs or drug-related grade 5 TEAEs. CONCLUSION The efficacy results of this study do not support further evaluation of regorafenib combined with nivolumab in GBM/AA. The safety profile was acceptable and manageable.
MODL-41. LOSS OF DISTAL CHROMOSOME 6Q AND ASSOCIATED <i>PDE10A</i> INDUCES AN AGGRESSIVE GLIOMA PHENOTYPE BY FACILITATING PRONEURAL TO MESENCHYMAL TRANSITION
Authors: Nicholas Nuechterlein, Allison Shelbourn, Neriah Alvinez, Frank Szulzewsky, Sonali Arora, Patrick Paddison, Leyre Merino-Galan, Siobhan Pattwell, Erik Sulman, Mi-Yeon Jung, Desmond Brown, Yeshavanth Kumar Banasavadi-Siddegowda, Kayen Tang, Sadhana Jackson, Stefan Stoica, Prashant Chittaboina, Anoop Patel, Eric Holland, Patrick Cimino, Linda Shapiro
Journal: Neuro-Oncology (2023)

Abstract Somatic copy number alterations (SCNAs) are common in glioblastoma, with some SCNAs having prognostic implications. Identifying and characterizing SCNA-related genes acting as oncogenes or tumor suppressors may potentially provide new therapeutic avenues for gliomas. In this study, we sought to uncover novel SCNA-related genes by employing an unbiased log rank analysis screen of genomic regions associated with glioblastoma survival. We identified 6q27 loss as an independent poorly-prognostic SCNA across three separate glioblastoma cohorts. An in vitro CRISPR screen using human neural stem cells identified five genes in the 6q27 region that caused increased cellular proliferation. One of these genes, phosphodiesterase 10A (PDE10A), had a gene dosage effect on expression and decreased expression in human and mouse glioma tumor tissue compared to normal brain, which are both common tumor suppressor phenotypes. Knockdown of Pde10a in mouse neural stem cells in vitro validated the human cell CRISPR screen phenotype. Suppression of Pde10a in RCAS/Tva mouse glioma in vivo caused decreased survival with increased tumor grade, mitotic activity, necrosis, Vegfa expression, and AKT/pS6 signaling. Single cell RNA-sequencing of mouse gliomas revealed that Pde10a suppression results in a shift from proneural to mesenchymal-like state. In human glioma tissue, PDE10A loss is also associated with an increased mesenchymal signature. Top activated pathways in Pde10a suppressed gliomas involved cell-cell interaction, including upregulation of cell adhesion molecules and downregulation of focal adhesion complex disassembly genes. Functional analysis in vitro confirmed that Pde10a suppression results in increased extracellular matrix adhesion and decreased migration. Relevant to standard glioblastoma treatment, PDE10A loss was associated with decreased MGMT promoter methylation, decreased DNA methyltransferase gene expression, and it potentiated radiation resistance in vitro. In summary, we leveraged several multiomic and experimental platforms to reveal PDE10A as a tumor suppressor in glioblastoma, predominantly by inducing a proneural to mesenchymal transition phenotype.
MODL-19. DEVELOPMENT OF A RECURRENT GLIOBLASTOMA MURINE MODEL FOLLOWING SURGICAL RESECTION: INVESTIGATING THE TUMOR-IMMUNE MICROENVIRONMENT TO EVALUATE NOVEL PERIOPERATIVE THERAPIES
Authors: Arabinda Das, Heather R Stephens, Joe Mark, Jeff Garrison, Penny Sekerak, Randy Baraso, Daniel G McDonald, Milad Yazdani, Cynthia A Welsh, Libby Kosnik Infinger, Ramin Eskandari, William A Vandergrift III, Abhay K Varma, Sunil J Patel, David Cachia, Alicia M Zukas, Scott M Lindhorst
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Most glioblastoma (GBM) patients experience tumor recurrence following standard-of-care treatment which includes tumor resection, radiation, and chemotherapy with concomitant and adjuvant temozolomide. Currently, no murine surgical GBM resection models to evaluate novel therapies exist and understanding of postsurgical tumor microenvironment (TME) has yet to be fully elucidated in pre-clinical GBM models. METHODS GL261 GBM cells were orthotopically implanted in C57BL/6 mice on day 1. On day 14, tumor resection was performed using the NICO Murine Neuroscience System, an automated, intraoperative, pre-clinical surgical resection system designed to minimize damage to surrounding tissue thus preventing the need for animal sacrifice. Standard T2-MRI and Terason uSmart 3200T ultrasound system were used to analyze tumor size following resection and recurrent growth. Immunological and biochemical assays were performed to explore local TME. RESULTS We observed that surgically resected GL261 GBM mice survived 55 + 8 days whereas mice with unresected GBM survived 35 + 7 days following tumor implantation. This new preclinical surgical resection recurrent immunocompetent GBM (Sur-rGBM) model was used for analyzing TME. Our results demonstrated significant changes in TME, such as an increase in astrocytic activation (GFAP+), increased microglia/macrophage (CD11b+, and IBA-1+) infiltration to surrounding tissue, increase in M2 macrophage (TGM2+ and CCL22+) and NK regulatory cells (CDC 26 +), and increased angiogenesis (VEGF) in Sur-rGBM as compared to unresected GBM. We also observed increased proliferation (Ki-67) and upregulation of stem cell markers CD133, Nestin, and Olig2 at the protein level. CONCLUSION Our data demonstrated the upregulation of tumor-promoting activation factors in Sur-rGBM as compared to unresected GBM. Currently, the Sur-rGBM model does not fully resemble the entire treatment regimen offered to GBM patients. Thus, our future aim is to further refine this resection model and assess adjuvant therapies at different time points along disease progression without needing to sacrifice the animal for analysis of tissue.
RADT-25. IMPACT OF 18F-DOPA PET ON RADIATION TREATMENT PLANNING FROM PHASE II STUDY OF SHORT COURSE HYPOFRACTIONATED PROTON BEAM THERAPY FOR ELDERLY PATIENTS WITH GLIOBLASTOMA
Authors: Brady Laughlin, Deanna Pafundi, Matthew Buras, Jonathan Ashman, Bernard Bendok, Nadia Laack, William Breen, Michael Ruff, Anita Mahajan, Maciej Mrugala, Terence Sio, Joon Uhm, Ming Yang, Debra Brinkmann, Paul Brown, Leland Hu, Sujay Vora
Journal: Neuro-Oncology (2023)

Abstract PURPOSE 18F-DOPA is sensitive/specific for identifying areas of biologically aggressive disease for glioblastoma. We report the impact of 18F-DOPA on radiation treatment planning from a phase II study. METHODS Gross target volume (GTV) was defined by the boolean of high-risk PET (tumor/normal brain SUV &amp;gt; 2.0) and MRI T1 contrast enhancement (MRI-CE) including surgical cavity. The clinical target volume (CTV) included the GTV with 1cm margin. Using proton beam therapy, GTV ≤ 65 cc was treated with 25 (CTV), 30 (MRI-CE), and 35 (PET) GyE over 5 fractions with a simultaneous integrated boost. GTV &amp;gt; 65 cc received 30 (CTV), 35 (MRI-CE), and 40 (PET) GyE over 10 fractions. Radiation field design was compared to traditional 1.5cm CTV margin on MRI-CE. RESULTS Between May 2019 and October 2021, 39 patients were treated. The median MRI-CE tumor diameter was 5.2cm. The median PET volume was 7.9cc (range 0–64.9cc). The median MRI-CE volume was 35.1cc (range 8.6–114cc). High-risk PET was contained within: MRI-CE 18/39 (46%), MRI-CE + T2W FLAIR 13/39 (33%), MRI-CE + T2W FLAIR + outside GTV 4/39 (10%), outside GTV 2/39 (5%) and no uptake 2/39 (5%). Utilizing this planning technique, there was a 26% volume reduction in CTV to traditional 1.5 cm margin on MRI-CE. PET imaging in treatment planning allowed inclusion of high-risk disease that would have been excluded on traditional CTV in 23% of cases (range 1.6-33.8cc). PET was more predictive [HR 1.03 (95% CI 1.01, 1.05) p = 0.002] than MRI [HR 1.01 (95% CI 1.00, 1.03) p = 0.02] for death with each cc increasing risk of death by 3.1%. CONCLUSIONS The incorporation of 18F-DOPA in treatment planning yields a more targeted approach with reductions in both normal brain treated and risk of geographic miss compared to traditional CTV margins.
CTIM-27. PERIPHERAL BIOMARKER ANALYSIS OF T CELL-MEDIATED COLLAGEN REMODELING CORRELATES WITH TUMOR RESPONSES IN A PHASE IIA TRIAL OF VACCINE IMMUNOTHERAPEUTIC CANDIDATE (VBI-1901)
Authors: Fabio Iwamoto, Neel Nissen, David Reardon, Deborah Forst, Eudocia Lee, Tamara Berthoud, Catalina Soare, Francisco Diaz-Mitoma, David Anderson, Patrick Wen, Nicholas Willumsen, Morten Karsdal, Andrew Lassman
Journal: Neuro-Oncology (2023)

Abstract Cytomegalovirus (CMV) antigens have been reported in over 90% of GBMs. CD4+ and CD8+ T cells are most frequently directed against the gB and pp65 antigens, respectively, which are immunogenic targets in a CMV-based GBM immunotherapeutic. First-recurrent GBM patients with KPS³70 received VBI-1901 (a gB/pp65 enveloped virus-like particle [eVLP]) adjuvanted with GM-CSF intradermally (NCT03382977). Patients received VBI-1901 q4w, with serologic immune-monitoring q2w after each vaccination and surveillance brain MRI scans q6w. Among 16 patients treated with the highest (10µg dose) of VBI-1901, the mOS was 12.9 months with a 12-month OS rate of 62.5%. T cell-mediated collagen remodeling is necessary for T cell migration and activity. The peripheral C4G biomarker targets granzyme-B-cleaved type IV collagen, which is associated with T cell infiltration and has previously been shown to potentially identify recurrent GBM patients responding to nivolumab and bevacizumab. Here, C4G was measured in available plasma samples from patients with progressive disease (PD) (n = 9), stable disease (SD) (n = 5) or partial tumor responses (PR) (n = 2) prior to (baseline) and after (cycle 1-4) treatment with VBI-1901. Although numerically lower in patients with PD, there were no differences in baseline levels of C4G among the groups. However, there were statistically significant increases in C4G levels in the 2 patients with PR both after 1st/2nd doses (p = 0.0324) and after 3rd/4th doses (p = 0.0027) of treatment (1st/2nd doses; PD: 7.6ng/mL, SD: 10.0ng/mL, PR: 21.0ng/mL. 3rd/4th doses; PD: 6.1ng/mL, SD: 8.5ng/mL, PR: 16.8ng/mL). On-going analyses are evaluating additional peripheral markers of tumor microenvironment (TME) remodeling. Evaluating the balance of immune infiltration vs. tumor cell growth in patients with brain tumors is challenging and these data suggest a means of assessing this dynamic using a peripheral biomarker. These data may be particularly useful in discerning pseudoprogression associated with T cell infiltration from tumor progression.
INNV-04. RAPID CLINICAL AND RADIOLOGICAL RESPONSE TO BEVACIZUMAB IN A PATIENT WITH SCHWANNOMATOSIS
Authors: Maxim Yankelevich, Kaydee Kaiser, Karol Zakalik, Anant Krishnan, Joseph Fullmer
Journal: Neuro-Oncology (2023)

Abstract Limited evidence exists for optimal management of schwannomatosis, the least common neurofibromatosis syndrome characterized by multiple schwannomas and intractable pain in the absence of vestibular schwannomas and germline NF2 mutation. We present a case of a 32-year-old man with a family history of schwannomas who had been dealing with multiple paraspinal schwannomas throughout entire spine, neurological deficits and chronic severe pain since high school. He had multiple laminectomies with resection of schwannomas. By the time neurooncologist saw the patient he had been on daily narcotics for more than 10 years, was not ambulatory due to paraparesis and was dependent on chronic Foley catheter for urination. He was found to have SMARCB1 c.93G &amp;gt;A germline mutation that has not been reported before. Total spine MRI demonstrated further progression of multiple spinal schwannomas with cord compression. The patient started on bevacizumab 10 mg/kg IV every 4 weeks (the first dose 5 mg/kg) but had to have an 8-week interval between his second and third cycle because of slowly healing pressure ulcers over bilateral upper buttocks. The patient started to show improvement in leg movements and strength after 2 cycles, his urinary catheter was discontinued, and he started urinating on his own after 3 cycles of bevacizumab. MRI obtained after 3 cycles demonstrated decreasing size and enhancement of multiple schwannomas. The patient continued bevacizumab every 4 – 6 weeks and continued with clinical improvement of strength and mobility. He started to stand with support for several minutes after 6 cycles of bevacizumab and reported better control of pain. He started outpatient physical therapy sessions. The plan is to continue bevacizumab therapy long term. This case demonstrated efficacy of bevacizumab as an alternative treatment option to improve quality of life and avoid surgeries in patients with this rare debilitating condition.